Software Trapping: A Strategy for Finding Genes in Large Genomic Regions

• Published in: Computers and biomedical research Vol. 28; no. 2; pp. 140 - 153
• Main Authors: Kamb, Alexander, Wang, Chunwei, Thomas, Alun, DeHoff, Bradley S., Norris, Franklin H., Richardson, Katherine, Rine, Jasper, Skolnick, Mark H., Rosteck, Paul R.
• Format: Journal Article
• Language: English
• Published: San Diego, CA Elsevier Inc 01.04.1995; Academic Press
• Subjects: Bacteriophage P1 - genetics; Biological and medical sciences; Cloning, Molecular; Computerized, statistical medical data processing and models in biomedicine; DNA, Viral - genetics; Evaluation Studies as Topic; Exons; Genetic Techniques - statistics & numerical data; Genome; Medical computing and teaching; Medical sciences; Sensitivity and Specificity; Software; Characterization; Graphics; Biomedical data processing; Trapping; Gene; DNA; Software; Molecular biology
• ISSN: 0010-4809; 1090-2368
• DOI: 10.1006/cbmr.1995.1010

We present an approach to the gene identification phase of positional cloning that combines sparse sampling of DNA sequences from large genomic regions with computational analysis. We call the method "software trapping." The goal is to find coding exons while avoiding massive DNA sequence determination and contig assembly. Instead, rapid sequence sampling is combined with exon screening software such as a newly developed package called XPOUND to identify coding sequences. We have tested the approach using a set of model genomic sequences with known intron/exon structures as well as with bona fide P1 genomic clones. The results suggest that the strategy is a useful complement to other methods for finding genes in poorly characterized regions of genomes.